/**
 * PHOSIDE: PHosphorylation Site IDentification Engine.
 * Copyright 2009 Digital Biology Lab, University of Missouri.
 * This library is free software; you can redistribute it and/or modify it under
 * the terms of the GNU General Public License as published by the Free Software
 * Foundation; either version 3 of the License, or (at your option) any later
 * version. <p/> This library is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the License for more
 * details.
 */

package phoside.disorder;

import phoside.io.fasta.parser.DefaultHeaderParser;
import phoside.io.fasta.parser.HeaderParser;
import phoside.io.fasta.parser.HeaderRule;
import phoside.io.fasta.util.FastaVisitor;

import java.util.List;
import java.util.Map;

/**
 *
 * @author gjj
 */
public class DisorderPredictionFastaVisitor implements FastaVisitor {

    private final Map<String,List<Double>> mapAccDisorder;
    private final HeaderParser parser;
    private final DisorderPredictor predictor;

    public DisorderPredictionFastaVisitor(final Map<String,List<Double>> mapAccDisorder,
                                          final HeaderRule rule,
                                          final DisorderPredictor predictor) {
        if (mapAccDisorder==null || rule==null || predictor==null) {
            throw new NullPointerException();
        }

        this.mapAccDisorder = mapAccDisorder;
        parser = new DefaultHeaderParser(rule);
        this.predictor = predictor;
    }

    /**
     * 
     * @param header
     * @param sequence
     */
    public void visit(final String header, final String sequence) {
        if (header==null || sequence==null) {
            throw new NullPointerException("Null header or sequence.");
        }

        parser.parse(header);
        String accession = parser.getAccession();
        if (accession != null) {
            String seq;

            // remove * in the end
            if (sequence.endsWith("*")) {
                seq = sequence.substring(0,sequence.length()-1);
            } else {
                seq = sequence;
            }

            List<Double> res = predictor.predict(seq);
            if (res != null) {
                mapAccDisorder.put(accession, res);
            }
        }
    }

}
